JAL will only pull up the reservation if there is at least 1 JL-coded flight. Even then, they do not allow seat selection on JL flights with other airlines' numbers (like AA*JL). You have to reach out to AA for seat selection, special meals, etc. They seem to be very particular that marketing carriers make requests, and would sometimes adamantly refuse to help you with anything if you call them.

Otherwise, a common reason JL's website doesn't work is if you didn't prepend the flight number with leading 0s. For JAL flight 4, sometimes you need to put in JL004 for the website to work